Jiri Hon
| Snapshot Date: 2025-06-18 13:25 -0400 (Wed, 18 Jun 2025) |
| git_url: https://git.bioconductor.org/packages/triplex |
| git_branch: devel |
| git_last_commit: 7c99430 |
| git_last_commit_date: 2025-04-15 10:23:57 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-06-19 12:04 -0400 (Thu, 19 Jun 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4810 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" | 4548 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" | 4528 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4493 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 2216/2309 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| triplex 1.49.0 (landing page) Jiri Hon
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the triplex package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/triplex.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: triplex |
| Version: 1.49.0 |
| Command: rm -rf triplex.buildbin-libdir && mkdir triplex.buildbin-libdir && F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL --build --library=triplex.buildbin-libdir triplex_1.49.0.tar.gz |
| StartedAt: 2025-06-19 10:21:25 -0400 (Thu, 19 Jun 2025) |
| EndedAt: 2025-06-19 10:22:23 -0400 (Thu, 19 Jun 2025) |
| EllapsedTime: 57.9 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: triplex_1.49.0.zip |
| PackageFileSize: 815.6 KiB |
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### Running command:
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### rm -rf triplex.buildbin-libdir && mkdir triplex.buildbin-libdir && F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL --build --library=triplex.buildbin-libdir triplex_1.49.0.tar.gz
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* installing *source* package 'triplex' ...
** this is package 'triplex' version '1.49.0'
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 14.2.0'
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c R_init_triplex.c -o R_init_triplex.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c align.c -o align.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c align_interface.c -o align_interface.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c dl_list.c -o dl_list.o
dl_list.c: In function 'dl_list_merge_sort':
dl_list.c:307:19: warning: 'act_start' may be used uninitialized [-Wmaybe-uninitialized]
307 | if ((act_start < min_start) ||
| ^
dl_list.c:283:41: note: 'act_start' was declared here
283 | int i, min_list, min_start, min_end, act_start, act_end, items = 0;
| ^~~~~~~~~
dl_list.c:308:46: warning: 'act_end' may be used uninitialized [-Wmaybe-uninitialized]
308 | ((act_start == min_start) && (act_end < min_end))){
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
dl_list.c:283:52: note: 'act_end' was declared here
283 | int i, min_list, min_start, min_end, act_start, act_end, items = 0;
| ^~~~~~~
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c interval.c -o interval.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c libtriplex.c -o libtriplex.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c progress.c -o progress.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c search.c -o search.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c search_interface.c -o search_interface.o
search_interface.c: In function 'decode_DNAString':
search_interface.c:371:84: warning: pointer used after 'free' [-Wuse-after-free]
371 | error("Unsupported symbol '%c' in input sequence.", dna.seq[i]);
| ^
search_interface.c:370:25: note: call to 'free' here
370 | free(dna.seq);
| ^~~~~~~~~~~~~
gcc -shared -s -static-libgcc -o triplex.dll tmp.def Biostrings_stubs.o IRanges_stubs.o R_init_triplex.o XVector_stubs.o align.o align_interface.o dl_list.o interval.o libtriplex.o progress.o search.o search_interface.o -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.22-bioc/meat/triplex.buildbin-libdir/00LOCK-triplex/00new/triplex/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'grid::pattern' by 'Biostrings::pattern' when loading 'triplex'
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'grid::pattern' by 'Biostrings::pattern' when loading 'triplex'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'grid::pattern' by 'Biostrings::pattern' when loading 'triplex'
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'triplex' as triplex_1.49.0.zip
* DONE (triplex)